Taxonomic analysis with percent
Preparation
Paths and libraries setting
# Load main packages, paths and custom functions
source("../../../source/main_packages.R")
source("../../../source/paths.R")
source("../../../source/functions.R")
# Load supplementary packages
packages <- c("RColorBrewer", "ggpubr", "cowplot")
invisible(lapply(packages, require, character.only = TRUE))Load phyloseq object after decontam
Parameters for plot
# new names for Genus
new_names_genus <- c("Wolbachia",
"Asaia",
"Legionella",
"Elizabethkingia",
"Chryseobacterium",
"Erwinia",
"Morganella",
"Pseudomonas",
"Delftia",
"Methylobacterium-Methylorubrum",
"Serratia",
"Coetzeea",
"NA"
)
# col for Genus
col_genus <- c("Wolbachia"="#FEB24C",
"Asaia"="#10E015",
"Legionella"="#DE3F23",
"Elizabethkingia"="#66A7ED",
"Chryseobacterium"="#F899FF",
"Erwinia"="#FFE352",
"Morganella"="#F5E4D3",
"Pseudomonas"="#DBF5F0",
"Delftia"="#C7C5B7",
"Methylobacterium-Methylorubrum"="blue",
"Serratia"="#B136F5",
"Coetzeea"="red",
"NA"="grey")
# param for plot
guide_italics <- guides(fill = guide_legend(label.theme = element_text(size = 10, face = "italic", colour = "Black", angle = 0)))
# labels
make.italic <- function(x) as.expression(lapply(x, function(y) bquote(italic(.(y)))))
labels = c("Wolbachia"=make.italic("Wolbachia"),
"Asaia"=make.italic("Asaia"),
"Legionella"=make.italic("Legionella"),
"Elizabethkingia"=make.italic("Elizabethkingia"),
"Chryseobacterium"=make.italic("Chryseobacterium"),
"Erwinia"=make.italic("Erwinia"),
"Morganella"=make.italic("Morganella"),
"Pseudomonas"=make.italic("Pseudomonas"),
"Delftia"=make.italic("Delftia"),
"Methylobacterium-Methylorubrum"=make.italic("Methylobacterium-Methylorubrum"),
"Serratia"=make.italic("Serratia"),
"Coetzeea"=make.italic("Coetzeea"),
"NA"
)Create objects by species, organ, location
Culex pipiens
# Whole
## All
df_count_pipiens_w <- df_count[df_count$Species.x=="Culex pipiens" & df_count$Organ=="Whole",]
## Field
df_count_pipiens_bosc_w <- df_count_pipiens_w[df_count_pipiens_w$Location=="Bosc",]
df_count_pipiens_ce_w <- df_count_pipiens_w[df_count_pipiens_w$Location=="Camping Europe",]
## Lab
df_count_pipiens_lavar_w <- df_count_pipiens_w[df_count_pipiens_w$Location=="Lavar (labo)",]
# Ovary
## All
df_count_pipiens_o <- df_count[df_count$Species.x=="Culex pipiens" & df_count$Organ=="Ovary",]
## Field
df_count_pipiens_bosc_o <- df_count_pipiens_o[df_count_pipiens_o$Location=="Bosc",]
df_count_pipiens_ce_o <- df_count_pipiens_o[df_count_pipiens_o$Location=="Camping Europe",]
## Lab
df_count_pipiens_lavar_o <- df_count_pipiens_o[df_count_pipiens_o$Location=="Lavar (labo)",]Culex quinquefasciatus
# Whole
## All
df_count_quinque_w <- df_count[df_count$Species.x=="Culex quinquefasciatus" & df_count$Organ=="Whole",]
## Field
df_count_quinque_g_w <- df_count_quinque_w[df_count_quinque_w$Location=="Guadeloupe",]
## Lab
df_count_quinque_lab_w <- df_count_quinque_w[df_count_quinque_w$Location=="Wolbachia -",]
# Ovary
## All
df_count_quinque_o <- df_count[df_count$Species.x=="Culex quinquefasciatus" & df_count$Organ=="Ovary",]
## Field
df_count_quinque_g_o <- df_count_quinque_o[df_count_quinque_o$Location=="Guadeloupe",]
## Lab
df_count_quinque_lab_o <- df_count_quinque_o[df_count_quinque_o$Location=="Wolbachia -",]Taxonomic plots (%)
Culex pipiens
# Whole
## All locations
pipiens1 <- percent_taxonomic_plot(df_count_pipiens_w, Species.x, "Culex pipiens", group="Genus", organ="Whole",new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
## Location by location
pipiens2 <- percent_taxonomic_plot(df_count_pipiens_bosc_w, Location, "Bosc", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
pipiens3 <- percent_taxonomic_plot(df_count_pipiens_ce_w, Location, "Camping Europe", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
pipiens4 <- percent_taxonomic_plot(df_count_pipiens_lavar_w, Location, "Lavar (labo)", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
pipiens4[["labels"]][["title"]] <- "Lavar (lab)"
# Ovary
pipiens5 <- percent_taxonomic_plot(df_count_pipiens_o, Species.x, "Culex pipiens", group="Genus", organ="Ovary", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(O)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
# Plot
p_pipiens <- plot_grid(pipiens1+ theme(legend.position="none"),
pipiens2+ theme(legend.position="none"),
pipiens3+ theme(legend.position="none"),
pipiens4+ theme(legend.position="none"),
pipiens5+ theme(legend.position="none", plot.margin = unit(c(0.17,-1,1.2,0), "cm")),
ncol = 5,
nrow = 2)
p_pipiens
Culex quinquefasciatus
# Whole
## All locations
quinque1<- percent_taxonomic_plot(df_count_quinque_w, Species.x, "Culex quinquefasciatus", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
## Location by location
quinque2 <- percent_taxonomic_plot(df_count_quinque_g_w, Location, "Guadeloupe", group="Genus", organ="Whole",new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
quinque3 <- percent_taxonomic_plot(df_count_quinque_lab_w, Location, "Wolbachia -", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
quinque3[["labels"]][["title"]] <- expression(paste(italic("Wolbachia"), "- (Slab TC)"))
# Ovary
quinque4 <- percent_taxonomic_plot(df_count_quinque_o, Species.x, "Culex quinquefasciatus", group="Genus", organ="Ovary", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(O)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
# Plot
p_quinque <- plot_grid(quinque1+ theme(legend.position="none"),
quinque2+ theme(legend.position="none"),
quinque3+ theme(legend.position="none"),
quinque4+ theme(legend.position="none", plot.margin = unit(c(0.17,0,1.2,0), "cm")),
plot.new(),
ncol = 5,
nrow = 2)
Aedes aegypti
# Whole
## All locations
aedes1 <- percent_taxonomic_plot(df_count_aedes_w, Species.x, "Aedes aegypti", group="Genus", organ="Whole", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(W)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
# Ovary
aedes2 <- percent_taxonomic_plot(df_count_aedes_o, Species.x, "Aedes aegypti", group="Genus", organ="Ovary", new_names=new_names_genus, col=col_genus, mylabels=labels)+
labs(tag = "(O)")+
theme(plot.tag.position = "topright")+
ylim(0, 110)
# Plot
p_aedes <- plot_grid(aedes1+ theme(legend.position="none"),
aedes2+ theme(legend.position="none", plot.margin = unit(c(0.17,0,1.2,0), "cm")),
plot.new(),
plot.new(),
plot.new(),
ncol = 5,
nrow = 2)
All
p_global <- plot_grid(pipiens1+ theme(legend.position="none"),
pipiens2+ theme(legend.position="none"),
pipiens3+ theme(legend.position="none"),
pipiens4+ theme(legend.position="none"),
pipiens5+ theme(legend.position="none", plot.margin = unit(c(0.17,1,1.2,0), "cm")),
quinque1+ theme(legend.position="none"),
quinque2+ theme(legend.position="none"),
quinque3+ theme(legend.position="none"),
quinque4+ theme(legend.position="none", plot.margin = unit(c(0.17,1,1.2,0), "cm")),
plot.new(),
aedes1+ theme(legend.position="none"),
aedes2+ theme(legend.position="none", plot.margin = unit(c(0.17,1,1.2,0), "cm")),
plot.new(),
plot.new(),
plot.new(),
nrow=3,
ncol=5
)+
draw_plot_label(c("A", "B", "C"), c(0, 0, 0), c(1, 2/3, 1/3), size = 15)
